[BUG] SQANTI filter not producing output

[sparthib]

Is there an existing issue for this?

• [X] I have searched the existing issues

Have you loaded the SQANTI3.env conda environment?

• [X] I have loaded the SQANTI3.env conda environment

Problem description

SQANTI filter mode not filtering both in rules or ML mode. I tried the very basic command on just the classification text file, in my log file I see "Running SQANTI3 filtering..." In the next step, it immediately seems to look for the inclusion-list.txt instead of running the rules or ML filter.

Code sample

python $SQANTI_DIR/sqanti3_filter.py rules $INPUT_DIR/all_samples_classification.txt python $SQANTI_DIR/sqanti3_filter.py ml $INPUT_DIR/all_samples_classification.txt

Error

Running SQANTI3 filtering...

Traceback (most recent call last):
  File "/users/sparthib/SQANTI3-5.2.1/sqanti3_filter.py", line 292, in <module>
    main()
  File "/users/sparthib/SQANTI3-5.2.1/sqanti3_filter.py", line 288, in main
    ids, inclusion_file = run_rules(args)
  File "/users/sparthib/SQANTI3-5.2.1/sqanti3_filter.py", line 146, in run_rules
    seqs_to_keep = set(line.strip() for line in open(inclusion_list))
FileNotFoundError: [Errno 2] No such file or directory: 'path_to_output/all_samples/sqanti3_qc/all_samples_inclusion-list.txt'
**** Job ends ****

Anything else?

No response

[Fabian-RY]

Hi @sparthib , thank you for using SQANTI3.

According to the error, it seems that at least one of the subdirectories in your path does not exist. Can you please check if the path and the file mentioned in the error exist ("path_to_output/all_samples/all_samples_inclusion-list.txt")? I

Thanks

[sparthib]

the issue turned out to be that the R script SQANTI3_rules_filter.R couldn't find the optparse library and I had to reinstall it in the environment. Thanks!